Er, um, as has been pointed out repeatedly in the past, Kawasaki Heavy Industries dwarfs Honda in total size. Honda just chooses to spend more on motorcycle racing and design/development.
Personally, I'm glad Honda blows so much money on bikes. If they didn't, who would? It also forces other manufacturers to spend money to stay competitive.
As for Honda's dominance of top-level GP racing... well, yeah, it does get a bit old after a while. It was great when KRJR won the championship on the Suzuki, but I guess that just wasn't meant to last.
I think the real issue is that Honda is the only manufacturer who *consistently* makes a competitive bike, so the very best riders, who could go anywhere, choose to go to Honda. Honda continues to win and get good publicity and good R&D from it, so they continue to pour money into it.
It's really a vicious cycle, not unlike the Montreal Canadiens dominance of North American hockey in the 50's and 60's.